src/jalview/jbgui/GAlignFrame.java

   1 /********************\r
   2  * 2004 Jalview Reengineered\r
   3  * Barton Group\r
   4  * Dundee University\r
   5  *\r
   6  * AM Waterhouse\r
   7  *******************/\r
   8 \r
   9 package jalview.jbgui;\r
  10 \r
  11 import javax.swing.*;\r
  12 import java.awt.event.*;\r
  13 import java.awt.*;\r
  14 \r
  15 public class GAlignFrame extends JInternalFrame\r
  16 {\r
  17   protected JMenuBar alignFrameMenuBar = new JMenuBar();\r
  18   protected JMenu fileMenu = new JMenu();\r
  19   protected JMenuItem closeMenuItem = new JMenuItem();\r
  20   protected JMenu editMenu = new JMenu();\r
  21   protected JMenu viewMenu = new JMenu();\r
  22   protected JMenu colourMenu = new JMenu();\r
  23   protected JMenu calculateMenu = new JMenu();\r
  24   protected JMenu alignMenu = new JMenu();\r
  25   protected JMenuItem groupsMenuItem = new JMenuItem();\r
  26   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();\r
  27   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();\r
  28   protected JMenuItem invertSequenceMenuItem = new JMenuItem();\r
  29   protected JMenuItem deselectAllColumnsMenuItem = new JMenuItem();\r
  30   protected JMenuItem remove2LeftMenuItem = new JMenuItem();\r
  31   protected JMenuItem remove2RightMenuItem = new JMenuItem();\r
  32   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();\r
  33   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();\r
  34   protected JMenuItem setGapCharMenuItem = new JMenuItem();\r
  35   protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();\r
  36   protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();\r
  37   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();\r
  38   protected JMenuItem sortIDMenuItem = new JMenuItem();\r
  39   protected JMenuItem sortGroupMenuItem = new JMenuItem();\r
  40   protected JMenuItem sortTreeOrderMenuItem = new JMenuItem();\r
  41   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();\r
  42   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();\r
  43   protected JMenuItem PCAMenuItem = new JMenuItem();\r
  44   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();\r
  45   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();\r
  46   protected JMenuItem clustalAlignMenuItem = new JMenuItem();\r
  47   BorderLayout borderLayout1 = new BorderLayout();\r
  48   public JLabel statusBar = new JLabel();\r
  49   protected JMenu saveAlignmentMenu = new JMenu();\r
  50   protected JMenu outputTextboxMenu = new JMenu();\r
  51   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
  52   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
  53   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
  54   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();\r
  55   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
  56   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
  57   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
  58   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
  59   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
  60   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
  61   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
  62   JMenuItem njTreeBlosumMenuItem = new JMenuItem();\r
  63   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();\r
  64   protected JCheckBoxMenuItem consensusGraphMenuItem = new JCheckBoxMenuItem();\r
  65   protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();\r
  66   JMenuItem htmlMenuItem = new JMenuItem();\r
  67   JMenuItem overviewMenuItem = new JMenuItem();\r
  68   protected JMenuItem undoMenuItem = new JMenuItem();\r
  69   protected JMenuItem redoMenuItem = new JMenuItem();\r
  70   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
  71   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
  72   protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();\r
  73   JMenuItem printMenuItem = new JMenuItem();\r
  74   protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();\r
  75   JMenuItem findMenuItem = new JMenuItem();\r
  76   JMenu searchMenu = new JMenu();\r
  77   protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();\r
  78   protected JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();\r
  79   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();\r
  80   JMenuItem deleteGroups = new JMenuItem();\r
  81   JMenuItem delete = new JMenuItem();\r
  82   JMenuItem copy = new JMenuItem();\r
  83   JMenuItem cut = new JMenuItem();\r
  84   JMenu jMenu1 = new JMenu();\r
  85   JMenuItem pasteNew = new JMenuItem();\r
  86   JMenuItem pasteThis = new JMenuItem();\r
  87   protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();\r
  88   JMenuItem createJPG = new JMenuItem();\r
  89   protected JMenuItem font = new JMenuItem();\r
  90   protected JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();\r
  91   public GAlignFrame()\r
  92   {\r
  93 \r
  94 \r
  95     try\r
  96     {\r
  97       jbInit();\r
  98       setJMenuBar(alignFrameMenuBar);\r
  99 \r
 100       JMenuItem item;\r
 101       // dynamically fill save as menu with available formats\r
 102       for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {\r
 103         item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));\r
 104         saveAlignmentMenu.add( item );\r
 105         item.addActionListener(new java.awt.event.ActionListener()\r
 106         {\r
 107           public void actionPerformed(ActionEvent e)\r
 108           {\r
 109             saveAs_actionPerformed(e);\r
 110           }\r
 111         });\r
 112 \r
 113         item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));\r
 114         item.addActionListener(new java.awt.event.ActionListener()\r
 115         {\r
 116           public void actionPerformed(ActionEvent e)\r
 117           {\r
 118             outputText_actionPerformed(e);\r
 119           }\r
 120         });\r
 121 \r
 122         outputTextboxMenu.add( item );\r
 123       }\r
 124 \r
 125     }\r
 126     catch(Exception e)\r
 127     {\r
 128       e.printStackTrace();\r
 129     }\r
 130 \r
 131     ButtonGroup colours = new ButtonGroup();\r
 132     colours.add(noColourmenuItem);\r
 133     colours.add(clustalColour);\r
 134     colours.add(zappoColour);\r
 135     colours.add(taylorColour);\r
 136     colours.add(hydrophobicityColour);\r
 137     colours.add(helixColour);\r
 138     colours.add(strandColour);\r
 139     colours.add(turnColour);\r
 140     colours.add(buriedColour);\r
 141     colours.add(userDefinedColour);\r
 142     colours.add(PIDColour);\r
 143     colours.add(BLOSUM62Colour);\r
 144     colours.add(nucleotideColour);\r
 145   }\r
 146   private void jbInit() throws Exception\r
 147   {\r
 148     fileMenu.setMnemonic('F');\r
 149     fileMenu.setText("File");\r
 150     saveAlignmentMenu.setMnemonic('L');\r
 151     saveAlignmentMenu.setText("Save alignment to local file");\r
 152     closeMenuItem.setMnemonic('C');\r
 153     closeMenuItem.setText("Close");\r
 154     closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 155     {\r
 156       public void actionPerformed(ActionEvent e)\r
 157       {\r
 158         closeMenuItem_actionPerformed(e);\r
 159       }\r
 160     });\r
 161     editMenu.setText("Edit");\r
 162     viewMenu.setText("View");\r
 163     colourMenu.setText("Colour");\r
 164     calculateMenu.setText("Calculate");\r
 165     alignMenu.setText("Web Service");\r
 166     groupsMenuItem.setVisible(false);\r
 167     groupsMenuItem.setText("Groups");\r
 168     groupsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 169     {\r
 170       public void actionPerformed(ActionEvent e)\r
 171       {\r
 172         groupsMenuItem_actionPerformed(e);\r
 173       }\r
 174     });\r
 175     selectAllSequenceMenuItem.setText("Select all");\r
 176     selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 177     {\r
 178       public void actionPerformed(ActionEvent e)\r
 179       {\r
 180         selectAllSequenceMenuItem_actionPerformed(e);\r
 181       }\r
 182     });\r
 183     deselectAllSequenceMenuItem.setText("Clear selection");\r
 184     deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 185     {\r
 186       public void actionPerformed(ActionEvent e)\r
 187       {\r
 188         deselectAllSequenceMenuItem_actionPerformed(e);\r
 189       }\r
 190     });\r
 191     invertSequenceMenuItem.setText("Invert sequence selection");\r
 192     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 193     {\r
 194       public void actionPerformed(ActionEvent e)\r
 195       {\r
 196         invertSequenceMenuItem_actionPerformed(e);\r
 197       }\r
 198     });\r
 199     deselectAllColumnsMenuItem.setText("Deselect all columns");\r
 200     deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 201     {\r
 202       public void actionPerformed(ActionEvent e)\r
 203       {\r
 204         deselectAllColumnsMenuItem_actionPerformed(e);\r
 205       }\r
 206     });\r
 207     remove2LeftMenuItem.setText("Remove sequence <- left of selected column");\r
 208     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 209     {\r
 210       public void actionPerformed(ActionEvent e)\r
 211       {\r
 212         remove2LeftMenuItem_actionPerformed(e);\r
 213       }\r
 214     });\r
 215     remove2RightMenuItem.setText("Remove sequence -> right of selected column");\r
 216     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 217     {\r
 218       public void actionPerformed(ActionEvent e)\r
 219       {\r
 220         remove2RightMenuItem_actionPerformed(e);\r
 221       }\r
 222     });\r
 223     removeGappedColumnMenuItem.setText("Remove gapped columns");\r
 224     removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 225     {\r
 226       public void actionPerformed(ActionEvent e)\r
 227       {\r
 228         removeGappedColumnMenuItem_actionPerformed(e);\r
 229       }\r
 230     });\r
 231     removeAllGapsMenuItem.setText("Remove all gaps");\r
 232     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 233     {\r
 234       public void actionPerformed(ActionEvent e)\r
 235       {\r
 236         removeAllGapsMenuItem_actionPerformed(e);\r
 237       }\r
 238     });\r
 239     setGapCharMenuItem.setText("Set gap character to \".\"");\r
 240     setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 241     {\r
 242       public void actionPerformed(ActionEvent e)\r
 243       {\r
 244         setGapCharMenuItem_actionPerformed(e);\r
 245       }\r
 246     });\r
 247     viewBoxesMenuItem.setText("Boxes");\r
 248     viewBoxesMenuItem.setState(true);\r
 249     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 250     {\r
 251       public void actionPerformed(ActionEvent e)\r
 252       {\r
 253         viewBoxesMenuItem_actionPerformed(e);\r
 254       }\r
 255     });\r
 256     viewTextMenuItem.setText("Text");\r
 257     viewTextMenuItem.setState(true);\r
 258     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 259     {\r
 260       public void actionPerformed(ActionEvent e)\r
 261       {\r
 262         viewTextMenuItem_actionPerformed(e);\r
 263       }\r
 264     });\r
 265     sortPairwiseMenuItem.setText("Sort by pairwise identity");\r
 266     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 267     {\r
 268       public void actionPerformed(ActionEvent e)\r
 269       {\r
 270         sortPairwiseMenuItem_actionPerformed(e);\r
 271       }\r
 272     });\r
 273     sortIDMenuItem.setText("Sort by ID");\r
 274     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 275     {\r
 276       public void actionPerformed(ActionEvent e)\r
 277       {\r
 278         sortIDMenuItem_actionPerformed(e);\r
 279       }\r
 280     });\r
 281     sortGroupMenuItem.setText("Sort by group");\r
 282     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 283     {\r
 284       public void actionPerformed(ActionEvent e)\r
 285       {\r
 286         sortGroupMenuItem_actionPerformed(e);\r
 287       }\r
 288     });\r
 289     sortTreeOrderMenuItem.setText("Sort by tree order");\r
 290     sortTreeOrderMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 291     {\r
 292       public void actionPerformed(ActionEvent e)\r
 293       {\r
 294         sortTreeOrderMenuItem_actionPerformed(e);\r
 295       }\r
 296     });\r
 297     removeRedundancyMenuItem.setText("Remove redundancy");\r
 298     removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 299     {\r
 300       public void actionPerformed(ActionEvent e)\r
 301       {\r
 302         removeRedundancyMenuItem_actionPerformed(e);\r
 303       }\r
 304     });\r
 305     pairwiseAlignmentMenuItem.setText("Pairwise alignments");\r
 306     pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 307     {\r
 308       public void actionPerformed(ActionEvent e)\r
 309       {\r
 310         pairwiseAlignmentMenuItem_actionPerformed(e);\r
 311       }\r
 312     });\r
 313     PCAMenuItem.setText("Principal component analysis");\r
 314     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 315     {\r
 316       public void actionPerformed(ActionEvent e)\r
 317       {\r
 318         PCAMenuItem_actionPerformed(e);\r
 319       }\r
 320     });\r
 321     averageDistanceTreeMenuItem.setText("Average distance tree using PID");\r
 322     averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 323     {\r
 324       public void actionPerformed(ActionEvent e)\r
 325       {\r
 326         averageDistanceTreeMenuItem_actionPerformed(e);\r
 327       }\r
 328     });\r
 329     neighbourTreeMenuItem.setText("Neighbour joining tree using PID");\r
 330     neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 331     {\r
 332       public void actionPerformed(ActionEvent e)\r
 333       {\r
 334         neighbourTreeMenuItem_actionPerformed(e);\r
 335       }\r
 336     });\r
 337     clustalAlignMenuItem.setText("Clustal alignment");\r
 338     clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 339     {\r
 340       public void actionPerformed(ActionEvent e)\r
 341       {\r
 342         clustalAlignMenuItem_actionPerformed(e);\r
 343       }\r
 344     });\r
 345     this.getContentPane().setLayout(borderLayout1);\r
 346     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 347     statusBar.setBackground(Color.white);\r
 348     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 349     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
 350     statusBar.setText("Status bar");\r
 351     outputTextboxMenu.setMnemonic('T');\r
 352     outputTextboxMenu.setText("Output alignment via textbox");\r
 353     clustalColour.setSelected(false);\r
 354     clustalColour.setText("Clustalx colours");\r
 355     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 356     {\r
 357       public void actionPerformed(ActionEvent e)\r
 358       {\r
 359         clustalColour_actionPerformed(e);\r
 360       }\r
 361     });\r
 362     zappoColour.setText("Zappo colour scheme");\r
 363     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 364     {\r
 365       public void actionPerformed(ActionEvent e)\r
 366       {\r
 367         zappoColour_actionPerformed(e);\r
 368       }\r
 369     });\r
 370     taylorColour.setText("Taylor colour scheme");\r
 371     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 372     {\r
 373       public void actionPerformed(ActionEvent e)\r
 374       {\r
 375         taylorColour_actionPerformed(e);\r
 376       }\r
 377     });\r
 378     hydrophobicityColour.setText("By hydrophobicity");\r
 379     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 380     {\r
 381       public void actionPerformed(ActionEvent e)\r
 382       {\r
 383         hydrophobicityColour_actionPerformed(e);\r
 384       }\r
 385     });\r
 386     helixColour.setText("Helix propensity");\r
 387     helixColour.addActionListener(new java.awt.event.ActionListener()\r
 388     {\r
 389       public void actionPerformed(ActionEvent e)\r
 390       {\r
 391         helixColour_actionPerformed(e);\r
 392       }\r
 393     });\r
 394     strandColour.setText("Strand propensity");\r
 395     strandColour.addActionListener(new java.awt.event.ActionListener()\r
 396     {\r
 397       public void actionPerformed(ActionEvent e)\r
 398       {\r
 399         strandColour_actionPerformed(e);\r
 400       }\r
 401     });\r
 402     turnColour.setText("Turn propensity");\r
 403     turnColour.addActionListener(new java.awt.event.ActionListener()\r
 404     {\r
 405       public void actionPerformed(ActionEvent e)\r
 406       {\r
 407         turnColour_actionPerformed(e);\r
 408       }\r
 409     });\r
 410     buriedColour.setText("Buried index");\r
 411     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 412     {\r
 413       public void actionPerformed(ActionEvent e)\r
 414       {\r
 415         buriedColour_actionPerformed(e);\r
 416       }\r
 417     });\r
 418     userDefinedColour.setText("User defined colours");\r
 419     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 420     {\r
 421       public void actionPerformed(ActionEvent e)\r
 422       {\r
 423         userDefinedColour_actionPerformed(e);\r
 424       }\r
 425     });\r
 426     PIDColour.setText("Percentage Identity");\r
 427     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 428     {\r
 429       public void actionPerformed(ActionEvent e)\r
 430       {\r
 431         PIDColour_actionPerformed(e);\r
 432       }\r
 433     });\r
 434     BLOSUM62Colour.setText("BLOSUM62 score");\r
 435     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 436     {\r
 437       public void actionPerformed(ActionEvent e)\r
 438       {\r
 439         BLOSUM62Colour_actionPerformed(e);\r
 440       }\r
 441     });\r
 442     avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");\r
 443     avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 444     {\r
 445       public void actionPerformed(ActionEvent e)\r
 446       {\r
 447         avTreeBlosumMenuItem_actionPerformed(e);\r
 448       }\r
 449     });\r
 450     njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");\r
 451     njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 452     {\r
 453       public void actionPerformed(ActionEvent e)\r
 454       {\r
 455         njTreeBlosumMenuItem_actionPerformed(e);\r
 456       }\r
 457     });\r
 458     consensusGraphMenuItem.setActionCommand("");\r
 459     consensusGraphMenuItem.setText("Consensus graph");\r
 460     consensusGraphMenuItem.setState(true);\r
 461     consensusGraphMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 462     {\r
 463       public void actionPerformed(ActionEvent e)\r
 464       {\r
 465         consensusGraphMenuItem_actionPerformed(e);\r
 466       }\r
 467     });\r
 468     colourTextMenuItem.setText("Colour text");\r
 469     colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 470     {\r
 471       public void actionPerformed(ActionEvent e)\r
 472       {\r
 473         colourTextMenuItem_actionPerformed(e);\r
 474       }\r
 475     });\r
 476     htmlMenuItem.setText("Output as HTML");\r
 477     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 478     {\r
 479       public void actionPerformed(ActionEvent e)\r
 480       {\r
 481         htmlMenuItem_actionPerformed(e);\r
 482       }\r
 483     });\r
 484     overviewMenuItem.setText("Overview window");\r
 485     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 486     {\r
 487       public void actionPerformed(ActionEvent e)\r
 488       {\r
 489         overviewMenuItem_actionPerformed(e);\r
 490       }\r
 491     });\r
 492     undoMenuItem.setEnabled(false);\r
 493     undoMenuItem.setMnemonic('Z');\r
 494     undoMenuItem.setText("Undo");\r
 495     undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 496     {\r
 497       public void actionPerformed(ActionEvent e)\r
 498       {\r
 499         undoMenuItem_actionPerformed(e);\r
 500       }\r
 501     });\r
 502     redoMenuItem.setEnabled(false);\r
 503     redoMenuItem.setMnemonic('0');\r
 504     redoMenuItem.setText("Redo");\r
 505     redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 506     {\r
 507       public void actionPerformed(ActionEvent e)\r
 508       {\r
 509         redoMenuItem_actionPerformed(e);\r
 510       }\r
 511     });\r
 512     conservationMenuItem.setText("By conservation");\r
 513     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 514     {\r
 515       public void actionPerformed(ActionEvent e)\r
 516       {\r
 517         conservationMenuItem_actionPerformed(e);\r
 518       }\r
 519     });\r
 520     noColourmenuItem.setText("None");\r
 521     noColourmenuItem.setSelected(true);\r
 522     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 523     {\r
 524       public void actionPerformed(ActionEvent e)\r
 525       {\r
 526         noColourmenuItem_actionPerformed(e);\r
 527       }\r
 528     });\r
 529     wrapMenuItem.setText("Wrap alignment");\r
 530     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 531     {\r
 532       public void actionPerformed(ActionEvent e)\r
 533       {\r
 534         wrapMenuItem_actionPerformed(e);\r
 535       }\r
 536     });\r
 537     printMenuItem.setText("Print");\r
 538     printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 539     {\r
 540       public void actionPerformed(ActionEvent e)\r
 541       {\r
 542         printMenuItem_actionPerformed(e);\r
 543       }\r
 544     });\r
 545     renderGapsMenuItem.setText("Render gaps");\r
 546     renderGapsMenuItem.setState(true);\r
 547     renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 548     {\r
 549       public void actionPerformed(ActionEvent e)\r
 550       {\r
 551         renderGapsMenuItem_actionPerformed(e);\r
 552       }\r
 553     });\r
 554     findMenuItem.setText("Find");\r
 555     findMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 556     {\r
 557       public void actionPerformed(ActionEvent e)\r
 558       {\r
 559         findMenuItem_actionPerformed(e);\r
 560       }\r
 561     });\r
 562     searchMenu.setText("Search");\r
 563 \r
 564     abovePIDThreshold.setText("Above PID threshold");\r
 565     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {\r
 566       public void actionPerformed(ActionEvent e) {\r
 567         abovePIDThreshold_actionPerformed(e);\r
 568       }\r
 569     });\r
 570     sequenceFeatures.setText("Sequence Features");\r
 571     sequenceFeatures.addActionListener(new ActionListener()\r
 572     {\r
 573       public void actionPerformed(ActionEvent actionEvent)\r
 574       {\r
 575         sequenceFeatures_actionPerformed(actionEvent);\r
 576       }\r
 577     });\r
 578     nucleotideColour.setText("Nucleotide colours");\r
 579     nucleotideColour.addActionListener(new java.awt.event.ActionListener()\r
 580     {\r
 581       public void actionPerformed(ActionEvent e)\r
 582       {\r
 583         nucleotideColour_actionPerformed(e);\r
 584       }\r
 585     });\r
 586     deleteGroups.setSelected(false);\r
 587     deleteGroups.setText("Delete all groups");\r
 588     deleteGroups.addActionListener(new java.awt.event.ActionListener()\r
 589     {\r
 590       public void actionPerformed(ActionEvent e)\r
 591       {\r
 592         deleteGroups_actionPerformed(e);\r
 593       }\r
 594     });\r
 595     copy.setText("Copy");\r
 596     copy.setMnemonic(KeyEvent.VK_C);\r
 597 \r
 598     copy.addActionListener(new java.awt.event.ActionListener()\r
 599     {\r
 600       public void actionPerformed(ActionEvent e)\r
 601       {\r
 602         copy_actionPerformed(e);\r
 603       }\r
 604     });\r
 605     cut.setText("Cut");\r
 606     cut.setMnemonic(KeyEvent.VK_X);\r
 607     cut.addActionListener(new java.awt.event.ActionListener()\r
 608     {\r
 609       public void actionPerformed(ActionEvent e)\r
 610       {\r
 611         cut_actionPerformed(e);\r
 612       }\r
 613     });\r
 614     delete.setText("Delete");\r
 615     delete.addActionListener(new java.awt.event.ActionListener()\r
 616     {\r
 617       public void actionPerformed(ActionEvent e)\r
 618       {\r
 619         delete_actionPerformed(e);\r
 620       }\r
 621     });\r
 622     jMenu1.setMnemonic('V');\r
 623     jMenu1.setText("Paste");\r
 624     pasteNew.setText("to new alignment");\r
 625     pasteNew.addActionListener(new java.awt.event.ActionListener()\r
 626     {\r
 627       public void actionPerformed(ActionEvent e)\r
 628       {\r
 629         pasteNew_actionPerformed(e);\r
 630       }\r
 631     });\r
 632     pasteThis.setText("add to this alignment");\r
 633     pasteThis.addActionListener(new java.awt.event.ActionListener()\r
 634     {\r
 635       public void actionPerformed(ActionEvent e)\r
 636       {\r
 637         pasteThis_actionPerformed(e);\r
 638       }\r
 639     });\r
 640     applyToAllGroups.setText("Apply colour to all groups");\r
 641     applyToAllGroups.setState(true);\r
 642     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()\r
 643     {\r
 644       public void actionPerformed(ActionEvent e)\r
 645       {\r
 646         applyToAllGroups_actionPerformed(e);\r
 647       }\r
 648     });\r
 649     createJPG.addActionListener(new java.awt.event.ActionListener()\r
 650     {\r
 651       public void actionPerformed(ActionEvent e)\r
 652       {\r
 653         createJPG_actionPerformed(e);\r
 654       }\r
 655     });\r
 656     createJPG.setText("Save as JPG Image");\r
 657     font.setText("Change Font");\r
 658     font.addActionListener(new java.awt.event.ActionListener()\r
 659     {\r
 660       public void actionPerformed(ActionEvent e)\r
 661       {\r
 662         font_actionPerformed(e);\r
 663       }\r
 664     });\r
 665     fullSeqId.setText("Show full sequence id");\r
 666     fullSeqId.addActionListener(new java.awt.event.ActionListener()\r
 667     {\r
 668       public void actionPerformed(ActionEvent e)\r
 669       {\r
 670         fullSeqId_actionPerformed(e);\r
 671       }\r
 672     });\r
 673     alignFrameMenuBar.add(fileMenu);\r
 674     alignFrameMenuBar.add(editMenu);\r
 675     alignFrameMenuBar.add(searchMenu);\r
 676     alignFrameMenuBar.add(viewMenu);\r
 677     alignFrameMenuBar.add(colourMenu);\r
 678     alignFrameMenuBar.add(calculateMenu);\r
 679     alignFrameMenuBar.add(alignMenu);\r
 680     fileMenu.add(saveAlignmentMenu);\r
 681     fileMenu.add(outputTextboxMenu);\r
 682     fileMenu.add(htmlMenuItem);\r
 683     fileMenu.add(createJPG);\r
 684     fileMenu.add(printMenuItem);\r
 685     fileMenu.addSeparator();\r
 686     fileMenu.add(closeMenuItem);\r
 687     editMenu.add(copy);\r
 688     editMenu.add(jMenu1);\r
 689     editMenu.add(cut);\r
 690     editMenu.add(delete);\r
 691     editMenu.addSeparator();\r
 692     editMenu.add(undoMenuItem);\r
 693     editMenu.add(redoMenuItem);\r
 694     editMenu.addSeparator();\r
 695     editMenu.add(deselectAllSequenceMenuItem);\r
 696     editMenu.add(selectAllSequenceMenuItem);\r
 697     editMenu.add(invertSequenceMenuItem);\r
 698     editMenu.add(deleteGroups);\r
 699     editMenu.add(groupsMenuItem);\r
 700     editMenu.addSeparator();\r
 701     editMenu.add(deselectAllColumnsMenuItem);\r
 702     editMenu.add(remove2LeftMenuItem);\r
 703     editMenu.add(remove2RightMenuItem);\r
 704     editMenu.addSeparator();\r
 705     editMenu.add(removeGappedColumnMenuItem);\r
 706     editMenu.add(removeAllGapsMenuItem);\r
 707     editMenu.add(setGapCharMenuItem);\r
 708     searchMenu.add(findMenuItem);\r
 709     viewMenu.add(font);\r
 710     viewMenu.add(fullSeqId);\r
 711     viewMenu.add(wrapMenuItem);\r
 712     viewMenu.add(viewBoxesMenuItem);\r
 713     viewMenu.add(viewTextMenuItem);\r
 714     viewMenu.add(colourTextMenuItem);\r
 715     viewMenu.add(renderGapsMenuItem);\r
 716     viewMenu.add(consensusGraphMenuItem);\r
 717     viewMenu.add(overviewMenuItem);\r
 718     viewMenu.add(sequenceFeatures);\r
 719     colourMenu.add(applyToAllGroups);\r
 720     colourMenu.add(noColourmenuItem);\r
 721     colourMenu.add(clustalColour);\r
 722     colourMenu.add(zappoColour);\r
 723     colourMenu.add(taylorColour);\r
 724     colourMenu.add(hydrophobicityColour);\r
 725     colourMenu.add(helixColour);\r
 726     colourMenu.add(strandColour);\r
 727     colourMenu.add(turnColour);\r
 728     colourMenu.add(buriedColour);\r
 729     colourMenu.add(nucleotideColour);\r
 730     colourMenu.add(userDefinedColour);\r
 731     colourMenu.add(PIDColour);\r
 732     colourMenu.add(BLOSUM62Colour);\r
 733     colourMenu.addSeparator();\r
 734     colourMenu.add(abovePIDThreshold);\r
 735     colourMenu.add(conservationMenuItem);\r
 736     calculateMenu.add(sortPairwiseMenuItem);\r
 737     calculateMenu.add(sortIDMenuItem);\r
 738     calculateMenu.add(sortGroupMenuItem);\r
 739     calculateMenu.add(sortTreeOrderMenuItem);\r
 740     calculateMenu.add(removeRedundancyMenuItem);\r
 741     calculateMenu.addSeparator();\r
 742     calculateMenu.add(pairwiseAlignmentMenuItem);\r
 743     calculateMenu.add(PCAMenuItem);\r
 744     calculateMenu.addSeparator();\r
 745     calculateMenu.add(averageDistanceTreeMenuItem);\r
 746     calculateMenu.add(neighbourTreeMenuItem);\r
 747     calculateMenu.add(avDistanceTreeBlosumMenuItem);\r
 748     calculateMenu.add(njTreeBlosumMenuItem);\r
 749     alignMenu.add(clustalAlignMenuItem);\r
 750     this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
 751     jMenu1.add(pasteNew);\r
 752     jMenu1.add(pasteThis);\r
 753   }\r
 754 \r
 755   protected void saveAs_actionPerformed(ActionEvent e)\r
 756   {\r
 757 \r
 758   }\r
 759 \r
 760   protected void outputText_actionPerformed(ActionEvent e)\r
 761   {\r
 762 \r
 763   }\r
 764 \r
 765   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
 766   {\r
 767 \r
 768   }\r
 769 \r
 770 \r
 771 \r
 772 \r
 773 \r
 774   protected void closeMenuItem_actionPerformed(ActionEvent e)\r
 775   {\r
 776 \r
 777   }\r
 778 \r
 779   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 780   {\r
 781 \r
 782   }\r
 783 \r
 784   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 785   {\r
 786 \r
 787   }\r
 788 \r
 789 \r
 790   protected void groupsMenuItem_actionPerformed(ActionEvent e)\r
 791   {\r
 792 \r
 793   }\r
 794 \r
 795 \r
 796   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 797   {\r
 798 \r
 799   }\r
 800 \r
 801   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 802   {\r
 803 \r
 804   }\r
 805 \r
 806   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 807   {\r
 808 \r
 809   }\r
 810 \r
 811 \r
 812   protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
 813   {\r
 814 \r
 815   }\r
 816 \r
 817   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 818   {\r
 819 \r
 820   }\r
 821 \r
 822   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 823   {\r
 824 \r
 825   }\r
 826 \r
 827   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 828   {\r
 829 \r
 830   }\r
 831 \r
 832   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 833   {\r
 834 \r
 835   }\r
 836 \r
 837   protected void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
 838   {\r
 839 \r
 840   }\r
 841 \r
 842 \r
 843 \r
 844 \r
 845 \r
 846   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 847   {\r
 848 \r
 849   }\r
 850 \r
 851 \r
 852   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 853   {\r
 854 \r
 855   }\r
 856 \r
 857   protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 858   {\r
 859 \r
 860   }\r
 861 \r
 862 \r
 863   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 864   {\r
 865 \r
 866   }\r
 867 \r
 868 \r
 869 \r
 870   protected void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
 871   {\r
 872 \r
 873   }\r
 874 \r
 875   protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
 876   {\r
 877 \r
 878   }\r
 879 \r
 880   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 881   {\r
 882 \r
 883   }\r
 884 \r
 885   protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 886   {\r
 887 \r
 888   }\r
 889 \r
 890   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 891   {\r
 892 \r
 893   }\r
 894 \r
 895   protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
 896   {\r
 897 \r
 898   }\r
 899 \r
 900   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 901   {\r
 902 \r
 903   }\r
 904 \r
 905   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 906   {\r
 907 \r
 908   }\r
 909 \r
 910   protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
 911   {\r
 912 \r
 913   }\r
 914 \r
 915   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
 916   {\r
 917 \r
 918   }\r
 919 \r
 920   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
 921   {\r
 922 \r
 923   }\r
 924 \r
 925 \r
 926   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 927   {\r
 928 \r
 929   }\r
 930 \r
 931   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 932   {\r
 933 \r
 934   }\r
 935 \r
 936 \r
 937 \r
 938   protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
 939   {\r
 940 \r
 941   }\r
 942 \r
 943 \r
 944 \r
 945 \r
 946   protected void clustalColour_actionPerformed(ActionEvent e)\r
 947   {\r
 948 \r
 949   }\r
 950 \r
 951   protected void zappoColour_actionPerformed(ActionEvent e)\r
 952   {\r
 953 \r
 954   }\r
 955 \r
 956   protected void taylorColour_actionPerformed(ActionEvent e)\r
 957   {\r
 958 \r
 959   }\r
 960 \r
 961 \r
 962   protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 963   {\r
 964 \r
 965   }\r
 966 \r
 967   protected void helixColour_actionPerformed(ActionEvent e)\r
 968   {\r
 969 \r
 970   }\r
 971 \r
 972   protected void strandColour_actionPerformed(ActionEvent e)\r
 973   {\r
 974 \r
 975   }\r
 976 \r
 977   protected void turnColour_actionPerformed(ActionEvent e)\r
 978   {\r
 979 \r
 980   }\r
 981 \r
 982   protected void buriedColour_actionPerformed(ActionEvent e)\r
 983   {\r
 984 \r
 985   }\r
 986 \r
 987 \r
 988 \r
 989   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
 990   {\r
 991 \r
 992   }\r
 993 \r
 994   protected void PIDColour_actionPerformed(ActionEvent e)\r
 995   {\r
 996 \r
 997   }\r
 998 \r
 999   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1000   {\r
1001 \r
1002   }\r
1003 \r
1004 \r
1005   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
1006   {\r
1007 \r
1008   }\r
1009 \r
1010   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
1011   {\r
1012 \r
1013   }\r
1014 \r
1015 \r
1016   protected void printMenuItem_actionPerformed(ActionEvent e)\r
1017   {\r
1018 \r
1019   }\r
1020 \r
1021   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
1022   {\r
1023 \r
1024   }\r
1025 \r
1026   protected void findMenuItem_actionPerformed(ActionEvent e)\r
1027   {\r
1028 \r
1029   }\r
1030 \r
1031 \r
1032   protected void abovePIDThreshold_actionPerformed(ActionEvent e) {\r
1033 \r
1034   }\r
1035 \r
1036   public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)\r
1037   {\r
1038 \r
1039   }\r
1040 \r
1041   protected void nucleotideColour_actionPerformed(ActionEvent e)\r
1042   {\r
1043 \r
1044   }\r
1045 \r
1046   protected void deleteGroups_actionPerformed(ActionEvent e)\r
1047   {\r
1048 \r
1049   }\r
1050 \r
1051  protected void copy_actionPerformed(ActionEvent e)\r
1052   {\r
1053 \r
1054   }\r
1055 \r
1056 \r
1057   protected void cut_actionPerformed(ActionEvent e)\r
1058   {\r
1059 \r
1060   }\r
1061 \r
1062   protected void delete_actionPerformed(ActionEvent e)\r
1063   {\r
1064 \r
1065   }\r
1066 \r
1067   protected void pasteNew_actionPerformed(ActionEvent e)\r
1068   {\r
1069 \r
1070   }\r
1071 \r
1072   protected void pasteThis_actionPerformed(ActionEvent e)\r
1073   {\r
1074 \r
1075   }\r
1076 \r
1077   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
1078   {\r
1079 \r
1080   }\r
1081 \r
1082   protected void createJPG_actionPerformed(ActionEvent e)\r
1083   {\r
1084 \r
1085   }\r
1086 \r
1087   protected void font_actionPerformed(ActionEvent e)\r
1088   {\r
1089 \r
1090   }\r
1091 \r
1092   protected void fullSeqId_actionPerformed(ActionEvent e)\r
1093   {\r
1094 \r
1095   }\r
1096 \r
1097 \r
1098 \r
1099 }\r